Bioinformatics Tutorial - Basic
生物信息学实践教程 - 基础篇

Teaching Philosophy

🎦 Study and Practice | 格物致知 知行合一
"Tell me and I forget. Teach me and I remember. Involve me and I learn." - Benjamin Franklin
We teach professional skills in bioinformatics. These skills are not just running software. They will give you the freedom of exploring various real data.

Aim

写在前面的话
相对于过去,突然地,我们发现数据不是太少而是太多,信息不是匮乏而是繁杂,新一代人的重要能力是“鉴别”和“挖掘”。
对生物信息学的工作而言,最重要的、最有用的基本工具和技能过去一直是,我相信很长一段时间也会始终是:
  1. 1.
    google
  2. 2.
    wikipedia
  3. 3.
    知乎
We aim to teach basic data skills that give you freedom.
  • Running bioinformatics software isn’t all that difficult, doesn’t take much skill, and it doesn’t embody any of the significant challenges of bioinformatics.…These data skills give you freedom
  • I believe these two qualities — reproducibility and robustness.
  • So what is a reproducible bioinformatics project? At the very least, it’s sharing your project’s code and data.
  • In wet lab biology, when experiments fail, it can be very apparent, but this is not always true in computing. Electrophoresis gels that look like Rorschach blots rather than tidy bands clearly indicate something went wrong. Unfortunately, without prior expectations, it can be quite difficult to distinguish good results from bad results.
  • The easy way to ensure everything is working properly is to adopt a cautious attitude , and check everything between computational steps.
  • You will almost certainly have to rerun an analysis more than once.
  • Write Code for Humans, Write Data for Computers
  • Use Existing Libraries Whenever Possible
  • Treat Data as Read-Only
  • Document Everything (-- Too geeky?) Just as a well-organized laboratory makes a scientist’s life easier, a well-organized and well-documented project makes a bioinformatician’s life easier.
-- <<Bioinformatics Data Skills>>

Major Authors

Yumin Zhu, Gang Xu, Zhuoer Dong, Yinghui Chen, Meifeng Zhou, Xupeng Chen, Xiaocheng Xi, Xi Hu, Jingyi Cao, Xiaofan Liu, Weihao Zhao, Siqi Wang and Zhi J. Lu
Section
Major Authors
Part I. Basic Skills
1.Setup
Zhi John Lu
1.1 Docker
Gang Xu/Yunfan Jin
1.2 Cluster
Gang Xu/Xiaofan Liu/Yunfan Jin
2.Linux
Zhi John Lu
2.1 Basic Command
Xi Hu
2.2 Practice Guide
Xi Hu/Zhuoer Dong
2.3 Linux Bash
Gang Xu
3.R
3.1 R Basics
Zhuoer Dong
3.2 Plot with R
Xiaochen Xi/Zhuoer Dong
4.Python
Yuhuan Tao
PART II. BASIC ANALYSES
1.Blast
Gang Xu
2.Conservation Analysis
Xi Hu
3.Function Analysis
3.1 GO
Gang Xu
3.2 KEGG
Gang Xu
3.3 GSEA
Zhuoer Dong

Contact Us

Copyright

Copyright © 2022 Lu Lab
2016-2022年于清华园
本书主要目的是用于清华大学本科生课《生物信息学导论》和博士生课《生物信息学实践》的上机指南。
Last modified 2mo ago